Multiple sequence alignment - TraesCS2A01G369400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G369400 chr2A 100.000 3009 0 0 1 3009 612307592 612304584 0.000000e+00 5557.0
1 TraesCS2A01G369400 chr2A 100.000 35 0 0 2385 2419 612304341 612304375 6.960000e-07 65.8
2 TraesCS2A01G369400 chr2D 92.065 2092 96 21 9 2086 470544239 470542204 0.000000e+00 2880.0
3 TraesCS2A01G369400 chr2B 90.596 1276 61 22 869 2103 549539906 549538649 0.000000e+00 1637.0
4 TraesCS2A01G369400 chr2B 85.110 544 49 14 1 529 549551947 549551421 7.390000e-146 527.0
5 TraesCS2A01G369400 chr2B 96.815 157 4 1 705 860 549540513 549540357 8.270000e-66 261.0
6 TraesCS2A01G369400 chr2B 90.000 130 9 4 584 713 549551406 549551281 6.670000e-37 165.0
7 TraesCS2A01G369400 chr7A 94.118 544 29 3 2463 3004 635366020 635366562 0.000000e+00 824.0
8 TraesCS2A01G369400 chr7A 93.502 277 15 3 2111 2385 635365555 635365830 2.790000e-110 409.0
9 TraesCS2A01G369400 chr3A 93.923 543 32 1 2463 3004 746977569 746977027 0.000000e+00 819.0
10 TraesCS2A01G369400 chr3A 93.684 285 15 3 2102 2385 746978041 746977759 9.970000e-115 424.0
11 TraesCS2A01G369400 chr3A 86.047 215 30 0 1198 1412 647499535 647499321 6.490000e-57 231.0
12 TraesCS2A01G369400 chr3A 78.061 392 61 23 1031 1416 647510175 647509803 1.090000e-54 224.0
13 TraesCS2A01G369400 chr3A 88.235 68 8 0 1031 1098 647499715 647499648 6.910000e-12 82.4
14 TraesCS2A01G369400 chr6B 93.738 543 31 2 2463 3004 706345038 706345578 0.000000e+00 811.0
15 TraesCS2A01G369400 chr6B 94.604 278 12 3 2111 2386 706344572 706344848 7.710000e-116 427.0
16 TraesCS2A01G369400 chr5B 93.186 543 35 2 2463 3004 507986243 507986784 0.000000e+00 797.0
17 TraesCS2A01G369400 chr5B 90.809 544 48 2 2463 3005 634352417 634351875 0.000000e+00 726.0
18 TraesCS2A01G369400 chr5B 94.386 285 12 4 2103 2386 507985773 507986054 4.610000e-118 435.0
19 TraesCS2A01G369400 chr5B 86.567 67 9 0 1031 1097 689646091 689646157 1.160000e-09 75.0
20 TraesCS2A01G369400 chr1D 92.647 544 36 3 2463 3004 223519094 223518553 0.000000e+00 780.0
21 TraesCS2A01G369400 chr1D 92.857 280 14 2 2111 2389 223519554 223519280 4.670000e-108 401.0
22 TraesCS2A01G369400 chr1D 83.710 221 36 0 1199 1419 462298914 462299134 3.040000e-50 209.0
23 TraesCS2A01G369400 chr4B 92.650 517 36 2 2463 2978 12116872 12117387 0.000000e+00 743.0
24 TraesCS2A01G369400 chr4B 94.909 275 11 3 2113 2386 12116411 12116683 7.710000e-116 427.0
25 TraesCS2A01G369400 chr4B 75.137 547 115 10 1201 1738 184241288 184240754 1.390000e-58 237.0
26 TraesCS2A01G369400 chr3D 78.692 413 75 11 1312 1722 551207510 551207911 2.300000e-66 263.0
27 TraesCS2A01G369400 chr3D 84.579 214 31 2 1200 1412 511444084 511443872 8.450000e-51 211.0
28 TraesCS2A01G369400 chr3D 84.091 220 32 3 1198 1416 511451198 511450981 3.040000e-50 209.0
29 TraesCS2A01G369400 chr3D 88.235 68 8 0 1031 1098 511444265 511444198 6.910000e-12 82.4
30 TraesCS2A01G369400 chr4D 75.686 547 112 10 1201 1738 121440478 121439944 1.380000e-63 254.0
31 TraesCS2A01G369400 chr3B 85.185 216 30 2 1198 1412 673097981 673097767 1.400000e-53 220.0
32 TraesCS2A01G369400 chr3B 84.141 227 32 4 1190 1414 673106350 673106126 1.820000e-52 217.0
33 TraesCS2A01G369400 chr3B 88.235 68 8 0 1031 1098 673098161 673098094 6.910000e-12 82.4
34 TraesCS2A01G369400 chr3B 86.301 73 10 0 1031 1103 673106484 673106412 2.490000e-11 80.5
35 TraesCS2A01G369400 chr1A 84.112 214 34 0 1199 1412 554083768 554083981 1.090000e-49 207.0
36 TraesCS2A01G369400 chr6D 85.405 185 27 0 2198 2382 72410424 72410608 3.060000e-45 193.0
37 TraesCS2A01G369400 chr7B 83.951 81 7 2 2785 2859 740566319 740566239 4.160000e-09 73.1
38 TraesCS2A01G369400 chr7B 82.716 81 8 2 2785 2859 740659586 740659506 1.940000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G369400 chr2A 612304584 612307592 3008 True 5557.0 5557 100.0000 1 3009 1 chr2A.!!$R1 3008
1 TraesCS2A01G369400 chr2D 470542204 470544239 2035 True 2880.0 2880 92.0650 9 2086 1 chr2D.!!$R1 2077
2 TraesCS2A01G369400 chr2B 549538649 549540513 1864 True 949.0 1637 93.7055 705 2103 2 chr2B.!!$R1 1398
3 TraesCS2A01G369400 chr2B 549551281 549551947 666 True 346.0 527 87.5550 1 713 2 chr2B.!!$R2 712
4 TraesCS2A01G369400 chr7A 635365555 635366562 1007 False 616.5 824 93.8100 2111 3004 2 chr7A.!!$F1 893
5 TraesCS2A01G369400 chr3A 746977027 746978041 1014 True 621.5 819 93.8035 2102 3004 2 chr3A.!!$R3 902
6 TraesCS2A01G369400 chr6B 706344572 706345578 1006 False 619.0 811 94.1710 2111 3004 2 chr6B.!!$F1 893
7 TraesCS2A01G369400 chr5B 634351875 634352417 542 True 726.0 726 90.8090 2463 3005 1 chr5B.!!$R1 542
8 TraesCS2A01G369400 chr5B 507985773 507986784 1011 False 616.0 797 93.7860 2103 3004 2 chr5B.!!$F2 901
9 TraesCS2A01G369400 chr1D 223518553 223519554 1001 True 590.5 780 92.7520 2111 3004 2 chr1D.!!$R1 893
10 TraesCS2A01G369400 chr4B 12116411 12117387 976 False 585.0 743 93.7795 2113 2978 2 chr4B.!!$F1 865
11 TraesCS2A01G369400 chr4B 184240754 184241288 534 True 237.0 237 75.1370 1201 1738 1 chr4B.!!$R1 537
12 TraesCS2A01G369400 chr4D 121439944 121440478 534 True 254.0 254 75.6860 1201 1738 1 chr4D.!!$R1 537

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
998 1462 0.963225 GTAGGCCGGAGAGGAGAATC 59.037 60.0 5.05 0.0 45.00 2.52 F
1043 1507 0.546747 ACCGTTGAGGGGAGATGGAA 60.547 55.0 0.00 0.0 46.96 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2511 0.093365 GACGTTCGGCGCGATTTTAA 59.907 50.0 12.1 0.0 46.11 1.52 R
2794 3418 0.606401 TGGGCGAGGCTTTTCTGAAG 60.606 55.0 0.0 0.0 0.00 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 9.760660 CTGAACATGACTAAAGTTAACATAAGC 57.239 33.333 8.61 0.00 0.00 3.09
78 79 9.869844 CTGTATGTACGTTTATAGGTGTAGTAC 57.130 37.037 0.00 0.00 35.07 2.73
127 132 7.009357 TGTTTAGAAAACGAAATTCAAAACGGG 59.991 33.333 0.00 0.00 0.00 5.28
137 142 6.584563 CGAAATTCAAAACGGGTATCACAATT 59.415 34.615 0.00 0.00 0.00 2.32
169 181 7.713507 TGTGGTATAGACATTATTCGGGAAAAG 59.286 37.037 0.00 0.00 0.00 2.27
191 203 5.001874 AGCTGTATATGCATCAGACAATGG 58.998 41.667 15.96 4.25 0.00 3.16
192 204 4.379186 GCTGTATATGCATCAGACAATGGC 60.379 45.833 15.96 9.29 0.00 4.40
193 205 4.716794 TGTATATGCATCAGACAATGGCA 58.283 39.130 0.19 0.00 0.00 4.92
194 206 5.131784 TGTATATGCATCAGACAATGGCAA 58.868 37.500 0.19 0.00 0.00 4.52
195 207 5.771165 TGTATATGCATCAGACAATGGCAAT 59.229 36.000 0.19 0.00 0.00 3.56
196 208 5.801531 ATATGCATCAGACAATGGCAATT 57.198 34.783 0.19 0.00 0.00 2.32
238 250 7.612677 ACGACTGTTATGAATAGGAAGAAGTT 58.387 34.615 0.00 0.00 0.00 2.66
339 352 8.056400 TGGGCTAAGCTTAAAGGTTATTAATCA 58.944 33.333 7.74 0.00 37.52 2.57
348 361 6.927294 AAAGGTTATTAATCAGAAGCCTCG 57.073 37.500 0.00 0.00 0.00 4.63
449 464 4.680702 GGAGACGACAAATCTACCCTTAC 58.319 47.826 0.00 0.00 0.00 2.34
464 479 7.880623 TCTACCCTTACTAGAGAACTACCAAT 58.119 38.462 0.00 0.00 0.00 3.16
489 504 4.222114 GTCTTTTGAGCCAAAATCTGACG 58.778 43.478 11.78 2.73 41.53 4.35
503 518 7.975616 CCAAAATCTGACGGATTCATACAAATT 59.024 33.333 9.96 0.00 43.17 1.82
535 550 8.208718 TCAACTAATACAACACATATTCCTGC 57.791 34.615 0.00 0.00 0.00 4.85
537 552 6.578944 ACTAATACAACACATATTCCTGCGA 58.421 36.000 0.00 0.00 0.00 5.10
538 553 7.045416 ACTAATACAACACATATTCCTGCGAA 58.955 34.615 0.00 0.00 0.00 4.70
539 554 6.751514 AATACAACACATATTCCTGCGAAA 57.248 33.333 0.00 0.00 0.00 3.46
540 555 6.751514 ATACAACACATATTCCTGCGAAAA 57.248 33.333 0.00 0.00 0.00 2.29
541 556 5.446143 ACAACACATATTCCTGCGAAAAA 57.554 34.783 0.00 0.00 0.00 1.94
719 734 2.347490 CGGCCAGCTTGTAGTGGT 59.653 61.111 2.24 0.00 36.10 4.16
728 743 2.830704 CTTGTAGTGGTCGGCCGTCC 62.831 65.000 31.20 31.20 37.67 4.79
755 770 2.899900 TGCTGCGTATCCCTTCATATCT 59.100 45.455 0.00 0.00 0.00 1.98
864 880 3.308323 ACGTACACGCTAGCTAAGTACTC 59.692 47.826 25.23 11.24 44.43 2.59
866 882 2.354259 ACACGCTAGCTAAGTACTCGT 58.646 47.619 13.93 0.00 0.00 4.18
867 883 3.525537 ACACGCTAGCTAAGTACTCGTA 58.474 45.455 13.93 0.00 0.00 3.43
973 1437 3.242155 CGTGGAGCTAGATATCGATCGAC 60.242 52.174 22.06 8.13 37.15 4.20
998 1462 0.963225 GTAGGCCGGAGAGGAGAATC 59.037 60.000 5.05 0.00 45.00 2.52
1043 1507 0.546747 ACCGTTGAGGGGAGATGGAA 60.547 55.000 0.00 0.00 46.96 3.53
1103 1567 2.027385 AGGGATCGGGTACGTACTTTC 58.973 52.381 24.07 14.92 41.85 2.62
1112 1576 3.119566 GGGTACGTACTTTCCTCTGAGTG 60.120 52.174 24.07 0.00 0.00 3.51
1114 1581 4.217118 GGTACGTACTTTCCTCTGAGTGAA 59.783 45.833 24.07 4.44 0.00 3.18
1115 1582 4.240175 ACGTACTTTCCTCTGAGTGAAC 57.760 45.455 3.66 0.00 0.00 3.18
1121 1588 4.141390 ACTTTCCTCTGAGTGAACACCATT 60.141 41.667 3.66 0.00 0.00 3.16
1127 1594 4.910195 TCTGAGTGAACACCATTTATGCT 58.090 39.130 1.11 0.00 0.00 3.79
1128 1595 6.048732 TCTGAGTGAACACCATTTATGCTA 57.951 37.500 1.11 0.00 0.00 3.49
1129 1596 6.653020 TCTGAGTGAACACCATTTATGCTAT 58.347 36.000 1.11 0.00 0.00 2.97
1149 1616 8.766000 TGCTATTATTACATGGGTGTTATACG 57.234 34.615 0.00 0.00 39.77 3.06
1150 1617 8.369424 TGCTATTATTACATGGGTGTTATACGT 58.631 33.333 0.00 0.00 39.77 3.57
1151 1618 9.211485 GCTATTATTACATGGGTGTTATACGTT 57.789 33.333 0.00 0.00 39.77 3.99
1161 1628 8.545420 CATGGGTGTTATACGTTATTACAGAAC 58.455 37.037 0.00 0.00 29.47 3.01
1370 1846 2.328319 GAGAGGGAGAAGCTCATGGAT 58.672 52.381 0.00 0.00 31.08 3.41
1378 1854 2.766263 AGAAGCTCATGGATACGGTGAA 59.234 45.455 0.00 0.00 42.51 3.18
1381 1857 1.491670 CTCATGGATACGGTGAAGCG 58.508 55.000 0.00 0.00 42.51 4.68
1625 2101 3.902086 GGCCTCGCCGTCTACTCC 61.902 72.222 0.00 0.00 39.62 3.85
1655 2131 1.078848 GGCGATGAACCAGCTCACT 60.079 57.895 0.00 0.00 0.00 3.41
1766 2266 8.924511 ACATGGTATTTGATCCCTTTATGTAG 57.075 34.615 0.00 0.00 0.00 2.74
1778 2278 5.059833 CCCTTTATGTAGCTGTGATCTTCC 58.940 45.833 0.00 0.00 0.00 3.46
1803 2309 4.571176 GGAGAAACTCCTTAATAACGGCTG 59.429 45.833 10.16 0.00 46.41 4.85
1824 2330 5.386019 GCTGTAACTTCGATTTCGTTTTTGC 60.386 40.000 0.00 0.00 40.80 3.68
2005 2511 4.530857 GGCGGACGCACCATAGCT 62.531 66.667 18.95 0.00 44.11 3.32
2029 2535 2.728427 ATCGCGCCGAACGTCCTATC 62.728 60.000 0.00 0.00 46.11 2.08
2031 2537 2.353145 CGCCGAACGTCCTATCCG 60.353 66.667 0.00 0.00 36.87 4.18
2032 2538 2.827051 CGCCGAACGTCCTATCCGA 61.827 63.158 0.00 0.00 36.87 4.55
2033 2539 1.658673 GCCGAACGTCCTATCCGAT 59.341 57.895 0.00 0.00 0.00 4.18
2034 2540 0.877071 GCCGAACGTCCTATCCGATA 59.123 55.000 0.00 0.00 0.00 2.92
2037 2543 3.796504 GCCGAACGTCCTATCCGATAAAA 60.797 47.826 0.00 0.00 0.00 1.52
2039 2545 4.207841 CCGAACGTCCTATCCGATAAAAAC 59.792 45.833 0.00 0.00 0.00 2.43
2040 2546 5.039333 CGAACGTCCTATCCGATAAAAACT 58.961 41.667 0.00 0.00 0.00 2.66
2042 2548 6.507456 CGAACGTCCTATCCGATAAAAACTTG 60.507 42.308 0.00 0.00 0.00 3.16
2044 2550 6.400568 ACGTCCTATCCGATAAAAACTTGAA 58.599 36.000 0.00 0.00 0.00 2.69
2045 2551 6.875195 ACGTCCTATCCGATAAAAACTTGAAA 59.125 34.615 0.00 0.00 0.00 2.69
2046 2552 7.388500 ACGTCCTATCCGATAAAAACTTGAAAA 59.612 33.333 0.00 0.00 0.00 2.29
2069 2575 4.581824 AGTCACATCATTCAAAGCTGTTGT 59.418 37.500 0.00 0.00 0.00 3.32
2103 2611 6.757897 AAATTGTGTCGAATCATACCATGT 57.242 33.333 0.00 0.00 0.00 3.21
2104 2612 7.857734 AAATTGTGTCGAATCATACCATGTA 57.142 32.000 0.00 0.00 0.00 2.29
2105 2613 7.482654 AATTGTGTCGAATCATACCATGTAG 57.517 36.000 0.00 0.00 0.00 2.74
2106 2614 5.592104 TGTGTCGAATCATACCATGTAGT 57.408 39.130 0.00 0.00 0.00 2.73
2107 2615 6.702716 TGTGTCGAATCATACCATGTAGTA 57.297 37.500 0.00 0.00 0.00 1.82
2108 2616 7.284919 TGTGTCGAATCATACCATGTAGTAT 57.715 36.000 0.00 0.00 33.10 2.12
2136 2644 3.441496 TTTTGGCAACTCAAGAGCTTG 57.559 42.857 0.00 3.87 41.71 4.01
2169 2677 5.082251 AGTAGGAGGATTACAACGAAACC 57.918 43.478 0.00 0.00 0.00 3.27
2209 2717 6.551227 AGGAAAGAAGGCATGTAATTAATCCC 59.449 38.462 0.00 0.00 0.00 3.85
2286 2794 2.818921 TGGCTTCCCTATGCACAAAAT 58.181 42.857 0.00 0.00 0.00 1.82
2321 2829 7.208064 ACTATTAAAACCTCCCATAAGCTCA 57.792 36.000 0.00 0.00 0.00 4.26
2333 2841 5.308759 TCCCATAAGCTCATTGATCTCATGA 59.691 40.000 2.77 0.00 0.00 3.07
2339 2847 5.250982 AGCTCATTGATCTCATGACAAACA 58.749 37.500 1.79 0.00 0.00 2.83
2384 2892 5.068855 TGAAATTTCAGAGTTGCACATTCCA 59.931 36.000 16.91 0.00 32.50 3.53
2385 2893 3.988379 TTTCAGAGTTGCACATTCCAC 57.012 42.857 0.00 0.00 0.00 4.02
2386 2894 2.636647 TCAGAGTTGCACATTCCACA 57.363 45.000 0.00 0.00 0.00 4.17
2387 2895 2.929641 TCAGAGTTGCACATTCCACAA 58.070 42.857 0.00 0.00 0.00 3.33
2388 2896 3.489355 TCAGAGTTGCACATTCCACAAT 58.511 40.909 0.00 0.00 0.00 2.71
2389 2897 4.650734 TCAGAGTTGCACATTCCACAATA 58.349 39.130 0.00 0.00 0.00 1.90
2390 2898 5.069318 TCAGAGTTGCACATTCCACAATAA 58.931 37.500 0.00 0.00 0.00 1.40
2392 2900 5.803461 CAGAGTTGCACATTCCACAATAATG 59.197 40.000 0.00 0.00 39.68 1.90
2394 2902 6.658816 AGAGTTGCACATTCCACAATAATGTA 59.341 34.615 1.46 0.00 43.84 2.29
2395 2903 6.855836 AGTTGCACATTCCACAATAATGTAG 58.144 36.000 1.46 0.00 43.84 2.74
2396 2904 6.434028 AGTTGCACATTCCACAATAATGTAGT 59.566 34.615 1.46 0.00 43.84 2.73
2397 2905 7.609918 AGTTGCACATTCCACAATAATGTAGTA 59.390 33.333 1.46 0.00 43.84 1.82
2398 2906 7.552458 TGCACATTCCACAATAATGTAGTAG 57.448 36.000 1.46 0.00 43.84 2.57
2399 2907 7.109501 TGCACATTCCACAATAATGTAGTAGT 58.890 34.615 1.46 0.00 43.84 2.73
2400 2908 8.261522 TGCACATTCCACAATAATGTAGTAGTA 58.738 33.333 1.46 0.00 43.84 1.82
2401 2909 9.273016 GCACATTCCACAATAATGTAGTAGTAT 57.727 33.333 1.46 0.00 43.84 2.12
2437 2996 7.546667 ACAACACAATTCCATAATTTGAGCATC 59.453 33.333 0.00 0.00 32.87 3.91
2441 3000 7.434307 CACAATTCCATAATTTGAGCATCTGTC 59.566 37.037 0.00 0.00 32.87 3.51
2454 3013 2.420022 GCATCTGTCGCAAATTGGTACT 59.580 45.455 0.00 0.00 0.00 2.73
2455 3014 3.485877 GCATCTGTCGCAAATTGGTACTC 60.486 47.826 0.00 0.00 0.00 2.59
2458 3017 4.130857 TCTGTCGCAAATTGGTACTCAAA 58.869 39.130 0.00 0.00 39.05 2.69
2459 3018 4.213270 TCTGTCGCAAATTGGTACTCAAAG 59.787 41.667 0.00 0.00 39.05 2.77
2460 3019 4.130857 TGTCGCAAATTGGTACTCAAAGA 58.869 39.130 0.00 0.00 39.05 2.52
2461 3020 4.576873 TGTCGCAAATTGGTACTCAAAGAA 59.423 37.500 0.00 0.00 39.05 2.52
2537 3159 4.173256 GGTTGCCATAAAACTGTATGCAC 58.827 43.478 0.00 0.00 31.24 4.57
2538 3160 3.755965 TGCCATAAAACTGTATGCACG 57.244 42.857 0.00 0.00 31.24 5.34
2606 3228 0.392998 CTTTCCAGCGCCCACAGTAT 60.393 55.000 2.29 0.00 0.00 2.12
2624 3246 4.931601 CAGTATAGAAGCTTGCACTGAACA 59.068 41.667 2.10 0.00 36.37 3.18
2665 3287 5.336150 TCTAGCATTTCTCTCTGACCAAG 57.664 43.478 0.00 0.00 0.00 3.61
2759 3381 2.441750 TCCAAGTTTGAGGGTGTAGCTT 59.558 45.455 0.00 0.00 0.00 3.74
2770 3394 5.475564 TGAGGGTGTAGCTTTGGAATTTTAC 59.524 40.000 0.00 0.00 0.00 2.01
2771 3395 4.457949 AGGGTGTAGCTTTGGAATTTTACG 59.542 41.667 0.00 0.00 0.00 3.18
2794 3418 4.168760 CGATGCAACTTTCTTCATTTCCC 58.831 43.478 0.00 0.00 0.00 3.97
2796 3420 5.565439 CGATGCAACTTTCTTCATTTCCCTT 60.565 40.000 0.00 0.00 0.00 3.95
2808 3432 4.082125 TCATTTCCCTTCAGAAAAGCCTC 58.918 43.478 0.00 0.00 39.11 4.70
2876 3500 7.113658 TGCCACAAAATTTACAGAAAGGTAA 57.886 32.000 0.00 0.00 0.00 2.85
2894 3519 8.962884 AAAGGTAATTTCTCAATGTGCTTTTT 57.037 26.923 0.00 0.00 0.00 1.94
3005 3633 4.657814 TTTCCAGAAATTACCTCCAGCT 57.342 40.909 0.00 0.00 0.00 4.24
3006 3634 5.772393 TTTCCAGAAATTACCTCCAGCTA 57.228 39.130 0.00 0.00 0.00 3.32
3007 3635 5.359194 TTCCAGAAATTACCTCCAGCTAG 57.641 43.478 0.00 0.00 0.00 3.42
3008 3636 3.134804 TCCAGAAATTACCTCCAGCTAGC 59.865 47.826 6.62 6.62 0.00 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 9.222916 CTATAAACGTACATACAGTCAGAGTTG 57.777 37.037 0.00 0.00 0.00 3.16
106 107 5.001237 ACCCGTTTTGAATTTCGTTTTCT 57.999 34.783 0.00 0.00 0.00 2.52
124 129 1.064505 CAGCTGCAATTGTGATACCCG 59.935 52.381 0.00 0.00 0.00 5.28
127 132 2.489329 ACCACAGCTGCAATTGTGATAC 59.511 45.455 24.31 0.00 45.79 2.24
137 142 3.912496 AATGTCTATACCACAGCTGCA 57.088 42.857 15.27 0.00 0.00 4.41
169 181 4.379186 GCCATTGTCTGATGCATATACAGC 60.379 45.833 0.00 1.26 0.00 4.40
191 203 1.461897 GTCTTGCACATTGCCAATTGC 59.538 47.619 13.93 13.93 44.23 3.56
192 204 2.756829 TGTCTTGCACATTGCCAATTG 58.243 42.857 0.00 0.00 44.23 2.32
193 205 3.132925 GTTGTCTTGCACATTGCCAATT 58.867 40.909 0.00 0.00 44.23 2.32
194 206 2.758009 GTTGTCTTGCACATTGCCAAT 58.242 42.857 0.00 0.00 44.23 3.16
195 207 1.535649 CGTTGTCTTGCACATTGCCAA 60.536 47.619 0.00 0.00 44.23 4.52
196 208 0.030504 CGTTGTCTTGCACATTGCCA 59.969 50.000 0.00 0.00 44.23 4.92
197 209 0.310543 TCGTTGTCTTGCACATTGCC 59.689 50.000 0.00 0.00 44.23 4.52
246 259 4.820897 ACTGTGCGACATAAATCTGAAGA 58.179 39.130 0.00 0.00 0.00 2.87
247 260 4.033358 GGACTGTGCGACATAAATCTGAAG 59.967 45.833 0.00 0.00 0.00 3.02
325 338 5.823045 CCGAGGCTTCTGATTAATAACCTTT 59.177 40.000 0.00 0.00 0.00 3.11
326 339 5.368989 CCGAGGCTTCTGATTAATAACCTT 58.631 41.667 0.00 0.00 0.00 3.50
328 341 3.498777 GCCGAGGCTTCTGATTAATAACC 59.501 47.826 6.90 0.00 38.26 2.85
348 361 2.156098 TGTACTTGAATTCGGTTGGCC 58.844 47.619 0.00 0.00 0.00 5.36
402 415 6.344312 CGAGATTCAGTCGTAACGATTTCATC 60.344 42.308 0.00 0.00 38.42 2.92
418 433 2.921634 TTGTCGTCTCCGAGATTCAG 57.078 50.000 0.33 0.00 45.26 3.02
464 479 6.348458 CGTCAGATTTTGGCTCAAAAGACATA 60.348 38.462 19.29 9.04 44.72 2.29
551 566 9.440773 CCGTACATCCTACTACTACACAATATA 57.559 37.037 0.00 0.00 0.00 0.86
552 567 7.094463 GCCGTACATCCTACTACTACACAATAT 60.094 40.741 0.00 0.00 0.00 1.28
553 568 6.205464 GCCGTACATCCTACTACTACACAATA 59.795 42.308 0.00 0.00 0.00 1.90
554 569 5.009410 GCCGTACATCCTACTACTACACAAT 59.991 44.000 0.00 0.00 0.00 2.71
555 570 4.336433 GCCGTACATCCTACTACTACACAA 59.664 45.833 0.00 0.00 0.00 3.33
556 571 3.879295 GCCGTACATCCTACTACTACACA 59.121 47.826 0.00 0.00 0.00 3.72
557 572 3.879295 TGCCGTACATCCTACTACTACAC 59.121 47.826 0.00 0.00 0.00 2.90
558 573 4.155063 TGCCGTACATCCTACTACTACA 57.845 45.455 0.00 0.00 0.00 2.74
559 574 5.505173 TTTGCCGTACATCCTACTACTAC 57.495 43.478 0.00 0.00 0.00 2.73
560 575 6.528537 TTTTTGCCGTACATCCTACTACTA 57.471 37.500 0.00 0.00 0.00 1.82
561 576 5.410355 TTTTTGCCGTACATCCTACTACT 57.590 39.130 0.00 0.00 0.00 2.57
591 606 9.888878 CATGGAAAAGCATACAGTATATGAAAG 57.111 33.333 0.00 0.00 0.00 2.62
595 610 7.445096 TGTCCATGGAAAAGCATACAGTATATG 59.555 37.037 18.20 0.00 0.00 1.78
719 734 3.755628 GCACTACAGGACGGCCGA 61.756 66.667 35.90 7.04 39.96 5.54
728 743 0.747255 AGGGATACGCAGCACTACAG 59.253 55.000 0.00 0.00 37.60 2.74
755 770 1.176619 TTCGAGAACTCTGACGGCCA 61.177 55.000 2.24 0.00 0.00 5.36
767 782 0.944386 GCTGTTTGCCTGTTCGAGAA 59.056 50.000 0.00 0.00 35.15 2.87
864 880 8.393366 TCCGTGCTAGCTTATTTATAGTATACG 58.607 37.037 17.23 11.43 0.00 3.06
866 882 9.676861 TCTCCGTGCTAGCTTATTTATAGTATA 57.323 33.333 17.23 0.00 0.00 1.47
867 883 8.577048 TCTCCGTGCTAGCTTATTTATAGTAT 57.423 34.615 17.23 0.00 0.00 2.12
1025 1489 0.839946 ATTCCATCTCCCCTCAACGG 59.160 55.000 0.00 0.00 0.00 4.44
1027 1491 3.549794 CAAGATTCCATCTCCCCTCAAC 58.450 50.000 0.00 0.00 39.08 3.18
1029 1493 1.492176 GCAAGATTCCATCTCCCCTCA 59.508 52.381 0.00 0.00 39.08 3.86
1043 1507 4.473520 CCGTGGAGCCGGCAAGAT 62.474 66.667 31.54 7.63 41.78 2.40
1103 1567 4.095483 GCATAAATGGTGTTCACTCAGAGG 59.905 45.833 1.53 0.00 0.00 3.69
1114 1581 9.023962 CCCATGTAATAATAGCATAAATGGTGT 57.976 33.333 4.95 0.00 39.14 4.16
1115 1582 9.023962 ACCCATGTAATAATAGCATAAATGGTG 57.976 33.333 4.95 0.00 39.14 4.17
1145 1612 9.903682 ATACGCATTAGTTCTGTAATAACGTAT 57.096 29.630 13.05 13.05 39.50 3.06
1146 1613 9.172820 CATACGCATTAGTTCTGTAATAACGTA 57.827 33.333 0.00 10.77 39.00 3.57
1147 1614 7.703621 ACATACGCATTAGTTCTGTAATAACGT 59.296 33.333 0.00 0.00 37.73 3.99
1148 1615 8.057812 ACATACGCATTAGTTCTGTAATAACG 57.942 34.615 0.00 0.00 31.92 3.18
1152 1619 9.031360 CAAGTACATACGCATTAGTTCTGTAAT 57.969 33.333 0.00 0.00 0.00 1.89
1161 1628 4.511454 ACCATGCAAGTACATACGCATTAG 59.489 41.667 8.14 6.41 42.23 1.73
1165 1632 2.006169 CACCATGCAAGTACATACGCA 58.994 47.619 0.00 0.00 39.01 5.24
1370 1846 1.290955 CAGGGTTCGCTTCACCGTA 59.709 57.895 0.00 0.00 34.79 4.02
1625 2101 1.825191 CATCGCCCCCTTGGTCATG 60.825 63.158 0.00 0.00 36.04 3.07
1766 2266 3.006247 GTTTCTCCAGGAAGATCACAGC 58.994 50.000 0.00 0.00 35.16 4.40
1803 2309 4.899616 TCGCAAAAACGAAATCGAAGTTAC 59.100 37.500 10.16 0.00 43.02 2.50
1824 2330 0.317020 TATCTGCTCGACGCACATCG 60.317 55.000 5.59 0.00 45.47 3.84
2005 2511 0.093365 GACGTTCGGCGCGATTTTAA 59.907 50.000 12.10 0.00 46.11 1.52
2029 2535 7.860373 TGATGTGACTTTTCAAGTTTTTATCGG 59.140 33.333 0.00 0.00 43.03 4.18
2034 2540 9.434420 TTGAATGATGTGACTTTTCAAGTTTTT 57.566 25.926 0.00 0.00 43.03 1.94
2037 2543 7.223387 GCTTTGAATGATGTGACTTTTCAAGTT 59.777 33.333 0.00 0.00 43.03 2.66
2039 2545 6.921857 AGCTTTGAATGATGTGACTTTTCAAG 59.078 34.615 0.00 0.00 31.90 3.02
2040 2546 6.698329 CAGCTTTGAATGATGTGACTTTTCAA 59.302 34.615 0.00 0.00 31.90 2.69
2042 2548 6.211515 ACAGCTTTGAATGATGTGACTTTTC 58.788 36.000 1.02 0.00 32.51 2.29
2044 2550 5.779529 ACAGCTTTGAATGATGTGACTTT 57.220 34.783 1.02 0.00 32.51 2.66
2045 2551 5.068198 ACAACAGCTTTGAATGATGTGACTT 59.932 36.000 13.35 0.00 34.11 3.01
2046 2552 4.581824 ACAACAGCTTTGAATGATGTGACT 59.418 37.500 13.35 0.00 34.11 3.41
2047 2553 4.863491 ACAACAGCTTTGAATGATGTGAC 58.137 39.130 13.35 0.00 34.11 3.67
2048 2554 5.334028 CGTACAACAGCTTTGAATGATGTGA 60.334 40.000 13.35 0.00 34.69 3.58
2055 2561 6.811253 TTTATCCGTACAACAGCTTTGAAT 57.189 33.333 13.35 0.00 0.00 2.57
2087 2595 8.589335 AAACATACTACATGGTATGATTCGAC 57.411 34.615 21.76 0.00 46.97 4.20
2162 2670 2.029290 AGCTGATTGTACTCGGTTTCGT 60.029 45.455 0.00 0.00 37.69 3.85
2169 2677 5.250235 TCTTTCCTAGCTGATTGTACTCG 57.750 43.478 0.00 0.00 0.00 4.18
2209 2717 6.538021 CACAAAGGATAGAAGGAGATGTCTTG 59.462 42.308 0.00 0.00 0.00 3.02
2286 2794 9.070179 GGGAGGTTTTAATAGTTGTGTTCTTAA 57.930 33.333 0.00 0.00 0.00 1.85
2321 2829 4.142447 GCAGCTGTTTGTCATGAGATCAAT 60.142 41.667 16.64 0.00 0.00 2.57
2333 2841 2.555547 GGCCTTCGCAGCTGTTTGT 61.556 57.895 16.64 0.00 36.38 2.83
2339 2847 3.438017 GAGATCGGCCTTCGCAGCT 62.438 63.158 0.00 0.00 39.05 4.24
2406 2914 9.829507 TCAAATTATGGAATTGTGTTGTTTTCT 57.170 25.926 0.00 0.00 35.38 2.52
2408 2916 8.558700 GCTCAAATTATGGAATTGTGTTGTTTT 58.441 29.630 0.00 0.00 35.38 2.43
2410 2918 7.215789 TGCTCAAATTATGGAATTGTGTTGTT 58.784 30.769 0.00 0.00 35.38 2.83
2411 2919 6.757237 TGCTCAAATTATGGAATTGTGTTGT 58.243 32.000 0.00 0.00 35.38 3.32
2414 2922 7.093640 ACAGATGCTCAAATTATGGAATTGTGT 60.094 33.333 0.00 0.00 35.38 3.72
2415 2923 7.262772 ACAGATGCTCAAATTATGGAATTGTG 58.737 34.615 0.00 0.00 35.38 3.33
2437 2996 4.213270 TCTTTGAGTACCAATTTGCGACAG 59.787 41.667 0.00 0.00 34.23 3.51
2441 3000 5.460646 ACATTCTTTGAGTACCAATTTGCG 58.539 37.500 0.00 0.00 34.23 4.85
2454 3013 8.292448 GCTTCATTCTTTGAGTACATTCTTTGA 58.708 33.333 0.00 0.00 35.27 2.69
2455 3014 7.269937 CGCTTCATTCTTTGAGTACATTCTTTG 59.730 37.037 0.00 0.00 35.27 2.77
2458 3017 5.934625 ACGCTTCATTCTTTGAGTACATTCT 59.065 36.000 0.00 0.00 35.27 2.40
2459 3018 6.170675 ACGCTTCATTCTTTGAGTACATTC 57.829 37.500 0.00 0.00 35.27 2.67
2460 3019 5.122396 GGACGCTTCATTCTTTGAGTACATT 59.878 40.000 0.00 0.00 35.27 2.71
2461 3020 4.631813 GGACGCTTCATTCTTTGAGTACAT 59.368 41.667 0.00 0.00 35.27 2.29
2538 3160 2.093021 AGAGTCTAGACCTACGGTGACC 60.093 54.545 19.38 0.00 35.25 4.02
2602 3224 5.152623 TGTTCAGTGCAAGCTTCTATACT 57.847 39.130 0.00 0.00 0.00 2.12
2606 3228 4.388485 TGAATGTTCAGTGCAAGCTTCTA 58.612 39.130 0.00 0.00 32.50 2.10
2624 3246 6.054295 GCTAGAAGTCATGGTGAGAATGAAT 58.946 40.000 0.00 0.00 35.87 2.57
2759 3381 3.057876 AGTTGCATCGCGTAAAATTCCAA 60.058 39.130 5.77 0.00 0.00 3.53
2770 3394 2.532531 ATGAAGAAAGTTGCATCGCG 57.467 45.000 0.00 0.00 0.00 5.87
2771 3395 3.609807 GGAAATGAAGAAAGTTGCATCGC 59.390 43.478 0.00 0.00 0.00 4.58
2794 3418 0.606401 TGGGCGAGGCTTTTCTGAAG 60.606 55.000 0.00 0.00 0.00 3.02
2796 3420 0.606401 CTTGGGCGAGGCTTTTCTGA 60.606 55.000 0.00 0.00 0.00 3.27
2808 3432 3.921677 TCTCTTTTAGTGTACTTGGGCG 58.078 45.455 0.00 0.00 0.00 6.13
2876 3500 9.986833 GTTTTGTTAAAAAGCACATTGAGAAAT 57.013 25.926 0.00 0.00 35.96 2.17
2894 3519 0.665835 CGTGCAGGGCAGTTTTGTTA 59.334 50.000 0.00 0.00 40.08 2.41


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.